Towards an ontology of vector-borne diseases: MalIDO, the first step
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Transcript Towards an ontology of vector-borne diseases: MalIDO, the first step
Towards an ontology of vector-
borne diseases:
MalIDO, the first step.
Vector-borne diseases
Diseases transmitted to humans or
other animals through the bite of an
arthropod, usually an insect.
In contrast to most* other infectious
diseases it involves three organisms.
Insects and disease in the world (2001)
Disease
Deaths
DALYs
1,124
2,700
42,280
100,000
African trypanosomiasis
50
1,598
Chagas' disease
13
649
Leishmaniasis
59
2357
0
5,644
21
653
2,300
89,800
Malaria ("official" figures)
(estimated)
Lymphatic filariasis
Dengue fever, DHF, DHF-ss
AIDS
Numbers in Thousands; DALY: Disability-Adjusted Life Years
Insect- and arthropod-transmitted
diseases: a partial list
Malaria; African trypanosomiasis (sleeping disease);
American
trypanosomiasis
(Chagas’
disease);
Leishmaniasis; Lymphatic filariasis (several forms);
Dengue fever, DHF, DHF-SS; Yellow fever; Myiasis;
Onchocerciasis; Tungiasis; Bubonic plague; Relapsing
fever; various Encephalitides; Typhus; Lyme disease;
Japanese river fever; Urticaria; Loiasis; Dysenterrhoea;
various Dermatitides; and several more...
Vector-borne diseases:
Pathogens
(Arbo)Viruses (e.g. Dengue, Yellow fever, misc.
encephalitides, etc.)
Rickettsiae (e.g. Rocky Mountain spotted fever)
Bacteria (e.g. Bubonic plague, Lyme disease)
Protozoa (e.g. Malaria, Leishmaniasis, sleeping
disease, Chagas' disease)
Worms (e.g. Lymphatic filariasis, Onchocerciasis)
Insects (Myiasis)
Vector-borne diseases:
Vectors
Mosquitoes (e.g. Malaria, Lymphatic filariasis,
misc. encephalitides, Yellow fever, Dengue fever)
Sandflies (e.g. Leishmaniasis)
Ticks (e.g. Lyme disease, misc. encephalitides)
Blackflies (Onchocerciasis)
Tsetse (African trypanosomiasis)
Kissing bugs (American trypanosomiasis)
Fleas (Bubonic plague)
and a few more…
Vector-borne diseases:
Problems in disease control
Three organisms involved: Host (patient), vector,
pathogen.
Complicated epidemiology through vectors.
Vector-borne diseases:
Endemic countries
American & African
Trypanosomiasis
Dengue
Malaria
Lymphatic filariasis
Vector-borne diseases:
Endemic countries
Vector-borne diseases:
Endemic areas: tropics!
Vector-borne diseases:
Endemic areas: tropics!
Vector-borne diseases:
Endemic areas: tropics!
Vector-borne diseases:
Problems in disease control
Three organisms involved: Host (patient), vector,
pathogen.
Complicated epidemiology through vectors.
Mostly in the tropics.
Important factors: Poverty, geography,
insecticide resistance.
Vector-borne diseases:
Problems in disease control
Three organisms involved: Host (patient), vector,
pathogen.
Complicated epidemiology through vectors.
Mostly in the tropics.
Important factors: Poverty, geography,
insecticide and drug resistance.
Lack of vaccines with exception of Yellow fever.
Only build an ontology if:
You have a body of data to annotate.
You can think of good use cases.
You have community buy-in or can build that buy-in.
You commit to not wasting time on trivia.
You convince funders to pay for it.
You can take criticism.
You commit to being Open Source and encourage
community feedback.
[...] you can make annotated data available
You are pragmatic about technical issues.
You can commit to using the Relations Ontology.
You can commit to (re)-use community tools.
You are or are deemed to be “a person overly
obsessed
with minor details.”
From M. Ashburner (2007) IDO Workshop
Only build an ontology if:
You have a body of data to annotate.
You can think of good use cases.
You have community buy-in or can build that buy-in.
You commit to not wasting time on trivia.
You convince funders to pay for it.
You can take criticism.
You commit to being Open Source and encourage
community feedback.
[...] you can make annotated data available
You are pragmatic about technical issues.
You can commit to using the Relations Ontology.
You can commit to (re)-use community tools.
You are or are deemed to be “a person overly
obsessed
with minor details.”
From M. Ashburner (2007) IDO Workshop
Only build an ontology if:
You have a body of data to annotate.
You can think of good use cases.
You have community buy-in or can build that buy-in.
You commit to not wasting time on trivia.
You convince funders to pay for it.
You can take criticism.
You commit to being Open Source and encourage
community feedback.
[...] you can make annotated data available
You are pragmatic about technical issues.
You can commit to using the Relations Ontology.
You can commit to (re)-use community tools.
You are or are deemed to be “a person overly
obsessed
with minor details.”
WHO/Afro, EU/DGXII, IVCC
(Gates), MTC (Gates), PMI,
etc.
From M. Ashburner (2007) IDO Workshop
Ontologies at the IMBB
Assignment of GO terms to An. gambiae gene models (VectorBase).
Finished and passed over to ENSEMBL.
Construction of an ontology for the anatomy of mosquitoes. - Finished &
upgraded to CARO-compliancy, available through OBO (TGMA).
Construction of an ontology for the anatomy of ticks. - Finished, CAROcompliant, available through OBO (TADS), in collaboration with D.
Sonenshine.
Construction of an ontology addressing insecticide resistance. - Finished,
available through OBO (MIRO).
Construction of an ontology covering mosquito-specific physiological
processes. - In progress.
Construction of an ontology covering tick-specific phusiological processes.
- In progress, in collaboration with D. Sonenshine.
-
Vector-borne diseases:
Building an ontology
Use IDO as a "template”.
Vector-borne diseases:
Building an ontology
Use IDO as a "template”.
Single ontology for all, or different ones?
If different ones, based on vector, or pathogen,
or disease?
If based on disease, how specific (e.g. one or
four for malaria, what about filariasis)?
If based on vector, what balance to keep?
Vector-borne diseases:
Building MalIDO
Start with malaria and continue from there.
Use upper levels of IDO as much as possible.
Refine/edit MalIDO based on IDO's progress.
Include information on vectors as well, in
addition to pathogens and diseases.
Link MalIDO to existing ontologies.
Use MalIDO as a “template” for other
vector-borne diseases.
Vector-borne diseases:
Building MalIDO
Start with malaria and continue from there.
Use upper levels of IDO as much as possible.
Refine/edit MalIDO based on IDO's progress.
Include information on vectors as well, in
addition to pathogens and diseases.
Link MalIDO to existing ontologies.
Use MalIDO as a “template” for other
vector-borne diseases.
Vector-borne diseases:
Building MalIDO
Start with malaria and continue from there.
Use upper levels of IDO as much as possible.
Refine/edit MalIDO based on IDO's progress.
Include information on vectors as well, in
addition to pathogens and diseases.
Link MalIDO to existing ontologies.
Use MalIDO as a “template” for other
vector-borne diseases.
MalIDO:
Extended Info (12 September 2008)
Total terms = 1469
process has 1179 descendants
role has 103 descendants
quality has 131 descendants
object has 454 descendants
developmental stage has 25 descendants
object aggregate has 11 descendants
• terms with 0 parents: 6 (<1%)
• terms with 1 parents: 1364 (92%)
• terms with 2 parents: 85 (6%)
• terms with >2 parents: 1413 (<1%)
63% of terms have definitions (930 of 1469)
Insect- and arthropod-transmitted
diseases: a partial list
Malaria; African trypanosomiasis (sleeping disease);
American
trypanosomiasis
(Chagas’
disease);
Leishmaniasis; Lymphatic filariasis (several forms);
Dengue fever, DHF, DHF-SS; Yellow fever; Myiasis;
Onchocerciasis; Tungiasis; Bubonic plague; Relapsing
fever; various Encephalitides; Typhus; Lyme disease;
Japanese river fever; Urticaria; Loiasis; Dysenterrhoea;
various Dermatitides; and several more...
Manolis
Dialynas
Pantelis
Topalis
John
Vontas
IMBB-FORTH
???